Example 15. Applying different channel densities over a cell

Applying different channel densities over a cell. We start with a cell with a long axon, and then apply Hodgkin-Huxley channels over the surface. We look at the effect of changing the density of leak and sodium channels in just the axon of the neuron (not the soma)

This example also shows the use of tags; 300 traces are recorded in this experiment; but we don’t ever need to get involved in managing them directly. We can just specify that all traces recorded on simulation X should be tagged with “SIMY”, and then tell the TagViewer to plot everything with a tag ‘SIMY’

Code

from morphforge.stdimports import *
from morphforgecontrib.stdimports import StandardModels


def sim(glk_multiplier, gna_multiplier, tag):

    env = NEURONEnvironment()
    sim = env.Simulation()

    # Create a cell:
    morph = MorphologyBuilder.get_soma_axon_morph(axon_length=3000.0, axon_radius=0.3, soma_radius=9.0, axon_sections=20)
    cell = sim.create_cell(name="Cell1", morphology=morph)


    lk_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Lk", env=env)
    na_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Na", env=env)
    k_chl  = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="K", env=env)

    # Apply the channels uniformly over the cell
    cell.apply_channel(lk_chl)
    cell.apply_channel(na_chl)
    cell.apply_channel(k_chl)

    # Over-ride the parameters in the axon:
    cell.apply_channel(channel=lk_chl, where="axon", parameter_multipliers={'gScale':glk_multiplier})
    cell.apply_channel(channel=na_chl, where="axon", parameter_multipliers={'gScale':gna_multiplier})

    cell.set_passive( PassiveProperty.SpecificCapacitance, qty('1.0:uF/cm2'))


    for cell_location in CellLocator.get_locations_at_distances_away_from_dummy(cell=cell, distances=range(9, 3000, 100)):
        sim.record(cell, what=StandardTags.Voltage, cell_location=cell_location, user_tags=[tag])

    # Create the stimulus and record the injected current:
    cc = sim.create_currentclamp(name="Stim1", amp=qty("250:pA"), dur=qty("5:ms"), delay=qty("100:ms"), cell_location=cell.soma)
    sim.record(cc, what=StandardTags.Current)

    # run the simulation
    return sim.run()


# Display the results:
results_a = [
    sim(glk_multiplier=0.1, gna_multiplier=1.0, tag="SIM1"),
    sim(glk_multiplier=0.5, gna_multiplier=1.0, tag="SIM2"),
    sim(glk_multiplier=1.0, gna_multiplier=1.0, tag="SIM3"),
    sim(glk_multiplier=5.0, gna_multiplier=1.0, tag="SIM4"),
    sim(glk_multiplier=10.0, gna_multiplier=1.0, tag="SIM5"),
]

TagViewer(results_a, timerange=(97.5, 140)*units.ms, show=False,
          plots = [
                    TagPlot("ALL{Voltage,SIM1}", ylabel='gLeak: 0.1\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM2}", ylabel='gLeak: 0.5\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM3}", ylabel='gLeak: 1.0\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM4}", ylabel='gLeak: 5.0\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM5}", ylabel='gLeak: 10.0\nVoltage',yrange=(-80, 50)*units.mV, legend_labeller=None),
                       ])

results_b = [
    sim(gna_multiplier=0.1,  glk_multiplier=1.0, tag="SIM6"),
    sim(gna_multiplier=0.5,  glk_multiplier=1.0, tag="SIM7"),
    sim(gna_multiplier=0.75, glk_multiplier=1.0, tag="SIM8"),
    sim(gna_multiplier=1.0,  glk_multiplier=1.0, tag="SIM9"),
]

TagViewer(results_b, timerange=(97.5, 140)*units.ms, show=True,
          plots = [
                    TagPlot("ALL{Voltage,SIM6}", ylabel='gNa: 0.10\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM7}", ylabel='gNa: 0.50\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM8}", ylabel='gNa: 0.75\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM9}", ylabel='gNa: 1.00\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                       ])

Figures

../_images/singlecell_simulation080_out1.png

Download Figure

../_images/singlecell_simulation080_out2.png

Download Figure

Output

    No handlers could be found for logger "neurounits"
2013-12-01 17:11:58,226 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:11:58,226 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:12:00,529 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:00,529 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/37/37fe410751d68ab77348d725093b9a37.bundle (23k) : 0.843 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_af84455a7bd10be7408061ecd02b589b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_fb18cab9ab8db5d2c968f5e6fba6a942.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_250f079a9019e4d528955aa6190f2826.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_8be294eccf854380121f9cc2534c9637.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0491099357605
Running simulation : 2.325 seconds
Size of results file: 0.6 (MB)
Post-processing : 0.052 seconds
Entire load-run-save time : 3.221 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:05,427 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:05,427 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/9b/9ba409992e7a26e50ed93b6987b21266.bundle (23k) : 0.844 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_5c515003560d11f7f6c5bf95994063d3.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_21627
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_5c515003560d11f7f6c5bf95994063d3.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H   -I"."  -I".."  -I"/home/michael/opt//include/nrn"  -I"/home/michael/opt//x86_64/lib"    -g -O2 -c -o tmp_5c515003560d11f7f6c5bf95994063d3.lo tmp_5c515003560d11f7f6c5bf95994063d3.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module  -g -O2  -shared  -o tmp_5c515003560d11f7f6c5bf95994063d3.la  -rpath /home/michael/opt//x86_64/libs  tmp_5c515003560d11f7f6c5bf95994063d3.lo  -L/home/michael/opt//x86_64/lib -L/home/michael/opt//x86_64/lib  /home/michael/opt//x86_64/lib/libnrniv.la  -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
OP1: libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I/home/michael/opt//include/nrn -I/home/michael/opt//x86_64/lib -g -O2 -c tmp_5c515003560d11f7f6c5bf95994063d3.c  -fPIC -DPIC -o .libs/tmp_5c515003560d11f7f6c5bf95994063d3.o

OP2: libtool: link: gcc -shared  -fPIC -DPIC  .libs/tmp_5c515003560d11f7f6c5bf95994063d3.o   -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt/x86_64/lib/libnrniv.so /home/michael/opt/x86_64/lib/libnrnoc.so /home/michael/opt/x86_64/lib/liboc.so /home/michael/opt/x86_64/lib/libmemacs.so /home/michael/opt/x86_64/lib/libnrnmpi.so /home/michael/opt/x86_64/lib/libscopmath.so /home/michael/opt/x86_64/lib/libsparse13.so -lreadline -lncurses /home/michael/opt/x86_64/lib/libivoc.so /home/michael/opt/x86_64/lib/libneuron_gnu.so /home/michael/opt/x86_64/lib/libmeschach.so /home/michael/opt/x86_64/lib/libsundials.so -lm -ldl  -O2   -pthread -Wl,-soname -Wl,tmp_5c515003560d11f7f6c5bf95994063d3.so.0 -o .libs/tmp_5c515003560d11f7f6c5bf95994063d3.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_5c515003560d11f7f6c5bf95994063d3.so.0" && ln -s "tmp_5c515003560d11f7f6c5bf95994063d3.so.0.0.0" "tmp_5c515003560d11f7f6c5bf95994063d3.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_5c515003560d11f7f6c5bf95994063d3.so" && ln -s "tmp_5c515003560d11f7f6c5bf95994063d3.so.0.0.0" "tmp_5c515003560d11f7f6c5bf95994063d3.so")
libtool: link: ( cd ".libs" && rm -f "tmp_5c515003560d11f7f6c5bf95994063d3.la" && ln -s "../tmp_5c515003560d11f7f6c5bf95994063d3.la" "tmp_5c515003560d11f7f6c5bf95994063d3.la" )

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_9ecf8f39fd9146b277ff6177749299c6.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_62a4ddcd4ac772510aa6813825f854fa.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_979e51e8134d9ad14b8ff4498af4abcc.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_982d1751e1efe1e2df1ad423178619e6.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.053050994873
Running simulation : 3.140 seconds
Size of results file: 0.5 (MB)
Post-processing : 0.049 seconds
Entire load-run-save time : 4.033 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:11,057 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:11,057 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/b9/b9013013773c24d5cb34879f5a07e148.bundle (23k) : 0.834 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_1b9db84d43b77ec2fb2e53e206df6e31.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_08fd042f5617092e986b5453289c786a.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7df4c149812c25e673966e04c457447e.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_747cfe823e9c27c230ee7a5d068a636a.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.053318977356
Running simulation : 2.098 seconds
Size of results file: 0.4 (MB)
Post-processing : 0.042 seconds
Entire load-run-save time : 2.974 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:15,696 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:15,697 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/05/05ce1c77cbabd00648e2abc7f8391d8f.bundle (23k) : 0.873 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_441d00ac1d6ed2d478a432634287e05e.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_20f6d2c3344f354cb5e5fc2759b4552b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_493e4afc99901274d3bc57b05062327c.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_ab5326e2b7e5a80e09ceb3cda3d380a2.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0526940822601
Running simulation : 2.221 seconds
Size of results file: 0.5 (MB)
Post-processing : 0.048 seconds
Entire load-run-save time : 3.142 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:20,444 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:20,445 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/55/551abb27e0b05b74fe936ec535604fdb.bundle (23k) : 0.842 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_47e8f16ebc67f13d01a7bd84be614581.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_3bf774ddb40d01137fc04e1ccf2cc5ab.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_5163cbad7d6a5b01abf1db214c811de2.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_57e8f09677241bc3ffbeb65dd47e5da7.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0506639480591
Running simulation : 1.787 seconds
Size of results file: 0.4 (MB)
Post-processing : 0.039 seconds
Entire load-run-save time : 2.668 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:26,290 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:26,291 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/ee/eef320ba24fd739d08f1e52ea52b8bb4.bundle (23k) : 0.837 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_b251ce27fbf299b74853400c6fb7030f.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_9abe11266d08d5deb2ab5aadeb8cea7e.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7e273289d9d064fd79deb81dcb7d1f60.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_cef3a3ebf3889987f4800510c3b97a3b.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0505378246307
Running simulation : 1.485 seconds
Size of results file: 0.2 (MB)
Post-processing : 0.028 seconds
Entire load-run-save time : 2.351 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:30,214 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:30,215 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/49/49df28cc76631862075e306b4486c18a.bundle (23k) : 0.842 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_b251ce27fbf299b74853400c6fb7030f.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_9abe11266d08d5deb2ab5aadeb8cea7e.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7e273289d9d064fd79deb81dcb7d1f60.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_8d0569e097af1813e8d243c911b97f95.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0514340400696
Running simulation : 2.368 seconds
Size of results file: 0.5 (MB)
Post-processing : 0.048 seconds
Entire load-run-save time : 3.259 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:35,154 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:35,155 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/6a/6aa4576fdf0900bef97ea9ddd1ac210e.bundle (23k) : 0.836 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_1b9db84d43b77ec2fb2e53e206df6e31.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_08fd042f5617092e986b5453289c786a.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7df4c149812c25e673966e04c457447e.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_a3731a3d542f6133f77d4d744ce6fefb.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0515050888062
Running simulation : 2.148 seconds
Size of results file: 0.5 (MB)
Post-processing : 0.043 seconds
Entire load-run-save time : 3.027 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:39,802 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:39,803 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/5d/5d07db38cbcf52ca1b197aab262034d1.bundle (23k) : 0.833 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_441d00ac1d6ed2d478a432634287e05e.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_20f6d2c3344f354cb5e5fc2759b4552b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_493e4afc99901274d3bc57b05062327c.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_d13e0a86595a3af5720616e82c522fba.hoc
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Running Simulation
Time for Extracting Data: (30 records) 0.0521669387817
Running simulation : 2.084 seconds
Size of results file: 0.4 (MB)
Post-processing : 0.041 seconds
Entire load-run-save time : 2.959 seconds
Suceeded
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/37//37fe410751d68ab77348d725093b9a37.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/9b//9ba409992e7a26e50ed93b6987b21266.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/b9//b9013013773c24d5cb34879f5a07e148.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/05//05ce1c77cbabd00648e2abc7f8391d8f.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/55//551abb27e0b05b74fe936ec535604fdb.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/ee//eef320ba24fd739d08f1e52ea52b8bb4.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/49//49df28cc76631862075e306b4486c18a.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/6a//6aa4576fdf0900bef97ea9ddd1ac210e.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/5d//5d07db38cbcf52ca1b197aab262034d1.neuronsim.results.pickle ]
PlotManger saving:  _output/figures/singlecell_simulation080/{png,svg}/fig000_Autosave_figure_1.{png,svg}
PlotManger saving:  _output/figures/singlecell_simulation080/{png,svg}/fig001_Autosave_figure_2.{png,svg}